chr5-41586303-T-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000504215.1(ENSG00000251478):​n.1141A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000281 in 355,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000028 ( 0 hom. )

Consequence

ENSG00000251478
ENST00000504215.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.04

Publications

3 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TCP1P2 n.41586303T>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000251478ENST00000504215.1 linkn.1141A>T non_coding_transcript_exon_variant Exon 2 of 2 6
ENSG00000296840ENST00000742936.1 linkn.105-1238T>A intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000281
AC:
1
AN:
355366
Hom.:
0
Cov.:
0
AF XY:
0.00000529
AC XY:
1
AN XY:
189110
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
10452
American (AMR)
AF:
0.00
AC:
0
AN:
15216
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
10680
East Asian (EAS)
AF:
0.00
AC:
0
AN:
22510
South Asian (SAS)
AF:
0.00
AC:
0
AN:
41082
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
24594
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1478
European-Non Finnish (NFE)
AF:
0.00000478
AC:
1
AN:
209360
Other (OTH)
AF:
0.00
AC:
0
AN:
19994
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
CADD
Benign
1.7
DANN
Benign
0.36
PhyloP100
2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs583442; hg19: chr5-41586405; API